Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow¶

Autogenerated Report: RAINBOW Air-Liquid Interface Cell Culture Analysis¶

Website: https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI¶

Source directory¶

/mnt/hdd2/Alphons/Rainbow-Optical-Flow-For-ALI/examples/example_image_series/tif_191018_HNA-ALI_d14.nd2_-_191018_HNA-ALI_d14.nd2_(series_03)0000_etc

Image Series Type¶

.tif

RAINBOW Analysis Timestamp¶

10 March 2022, 15:57:34

Image Series Metadata¶

{
    "analysis_timestamp": "10 March 2022, 15:57:34",
    "calibration_um": 0.31302569743655434,
    "dir": "examples/example_image_series",
    "type": ".tif"
}

Magnitude Statistics¶

Out[7]:
frame min (um) max (um) mean (um) std (um) var (um)
0 0 0.001920 4.178234 2.138720 0.771738 0.595579
1 1 0.001551 3.935667 2.059078 0.799700 0.639520
2 2 0.102878 4.091494 2.039340 0.814543 0.663481
3 3 0.003530 3.479425 1.967105 0.759979 0.577568
4 4 0.004051 3.422691 1.889933 0.741848 0.550339
5 5 0.001329 3.128323 1.746436 0.634321 0.402363
6 6 0.005250 3.086464 1.701845 0.645827 0.417092
7 7 0.004330 3.372861 1.699563 0.644477 0.415350
8 8 0.002669 3.382966 1.754328 0.715596 0.512077
9 9 0.002633 3.494043 1.703855 0.734561 0.539580
10 10 0.003294 3.258862 1.729070 0.700330 0.490462
11 11 0.001932 3.233232 1.721925 0.726743 0.528155
12 12 0.000835 3.261815 1.664737 0.703804 0.495340
13 13 0.001779 3.125796 1.658646 0.718937 0.516870
14 14 0.002710 3.131470 1.644901 0.714538 0.510565
15 15 0.005129 3.323300 1.636716 0.735912 0.541567
16 16 0.001494 3.345547 1.656139 0.709268 0.503061
17 17 0.001446 3.342794 1.668112 0.729482 0.532144
18 18 0.000373 3.507166 1.661115 0.741280 0.549495

Direction Statistics¶

Out[8]:
frame min (deg) max (deg) mean (deg) std (deg) var (deg)
0 0 0.000098 360.000000 43.281408 42.713049 31.841866
1 1 0.000432 359.999237 35.513476 50.172646 43.935075
2 2 0.000003 359.999969 43.784291 50.391493 44.319190
3 3 0.000375 359.999969 36.392191 55.718097 54.183858
4 4 0.000753 359.999908 30.522460 63.856827 71.169193
5 5 0.000533 359.999969 34.993708 81.487163 115.892616
6 6 0.000154 359.999969 42.838753 88.519526 136.758879
7 7 0.000137 359.999969 29.267093 88.033618 135.261583
8 8 0.000022 359.999969 25.796501 83.577503 121.914723
9 9 0.000117 359.999725 18.781743 96.761745 163.412303
10 10 0.000212 359.999939 27.118338 92.455574 149.191323
11 11 0.000289 359.999878 10.934704 95.589848 159.478047
12 12 0.000058 359.999359 19.917708 100.345852 175.742263
13 13 0.000005 359.999786 38.717613 95.348774 158.674665
14 14 0.000228 359.998840 26.982311 95.167648 158.072397
15 15 0.000116 359.999878 45.586217 95.688977 159.808983
16 16 0.000045 359.999084 26.400442 93.869449 153.789224
17 17 0.000104 359.999969 47.943119 86.507444 130.612376
18 18 0.000290 359.999908 42.746733 95.632867 159.621621

Magnitude Scatter Plot¶

<Figure size 432x288 with 0 Axes>

Direction Scatter Plot¶

<Figure size 432x288 with 0 Axes>

Raw Image Series (left) and RAINBOW Optical Flow Visualisation (Right)¶

Out[15]:
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a) The direction of motion at any position within RAINBOW generated optical flow images is measured clockwise from the initial horizontal position of a unit circle (left) and is shown using hue values (right).

Key.png

Magnitude Heatmaps Across Image Series¶

Visualization of motion magnitiude using heatmap with hot colour mapping.

Out[17]:
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Quiver Plots Across Image Series¶

Visualisation of optical flow using quiver plots containing vector arrows.

Out[18]:
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Polar Plots Across Image Series¶

Visualisation of optical flow using polar plots.

Out[19]:
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